1
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Merlo G, Bachtel G, Sugden SG. Gut microbiota, nutrition, and mental health. Front Nutr 2024; 11:1337889. [PMID: 38406183 PMCID: PMC10884323 DOI: 10.3389/fnut.2024.1337889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
The human brain remains one of the greatest challenges for modern medicine, yet it is one of the most integral and sometimes overlooked aspects of medicine. The human brain consists of roughly 100 billion neurons, 100 trillion neuronal connections and consumes about 20-25% of the body's energy. Emerging evidence highlights that insufficient or inadequate nutrition is linked to an increased risk of brain health, mental health, and psychological functioning compromise. A core component of this relationship includes the intricate dynamics of the brain-gut-microbiota (BGM) system, which is a progressively recognized factor in the sphere of mental/brain health. The bidirectional relationship between the brain, gut, and gut microbiota along the BGM system not only affects nutrient absorption and utilization, but also it exerts substantial influence on cognitive processes, mood regulation, neuroplasticity, and other indices of mental/brain health. Neuroplasticity is the brain's capacity for adaptation and neural regeneration in response to stimuli. Understanding neuroplasticity and considering interventions that enhance the remarkable ability of the brain to change through experience constitutes a burgeoning area of research that has substantial potential for improving well-being, resilience, and overall brain health through optimal nutrition and lifestyle interventions. The nexus of lifestyle interventions and both academic and clinical perspectives of nutritional neuroscience emerges as a potent tool to enhance patient outcomes, proactively mitigate mental/brain health challenges, and improve the management and treatment of existing mental/brain health conditions by championing health-promoting dietary patterns, rectifying nutritional deficiencies, and seamlessly integrating nutrition-centered strategies into clinical care.
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Affiliation(s)
- Gia Merlo
- Department of Psychiatry, New York University Grossman School of Medicine and Rory Meyers College of Nursing, New York, NY, United States
| | | | - Steven G. Sugden
- Department of Psychiatry, The University of Utah School of Medicine, Salt Lake City, UT, United States
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2
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Voss G, Rosenthal JJC. High-level RNA editing diversifies the coleoid cephalopod brain proteome. Brief Funct Genomics 2023; 22:525-532. [PMID: 37981860 DOI: 10.1093/bfgp/elad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Coleoid cephalopods (octopus, squid and cuttlefish) have unusually complex nervous systems. The coleoid nervous system is also the only one currently known to recode the majority of expressed proteins through A-to-I RNA editing. The deamination of adenosine by adenosine deaminase acting on RNA (ADAR) enzymes produces inosine, which is interpreted as guanosine during translation. If this occurs in an open reading frame, which is the case for tens of thousands of editing sites in coleoids, it can recode the encoded protein. Here, we describe recent findings aimed at deciphering the mechanisms underlying high-level recoding and its adaptive potential. We describe the complement of ADAR enzymes in cephalopods, including a recently discovered novel domain in sqADAR1. We further summarize current evidence supporting an adaptive role of high-level RNA recoding in coleoids, and review recent studies showing that a large proportion of recoding sites is temperature-sensitive. Despite these new findings, the mechanisms governing the high level of RNA recoding in coleoid cephalopods remain poorly understood. Recent advances using genome editing in squid may provide useful tools to further study A-to-I RNA editing in these animals.
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Affiliation(s)
- Gjendine Voss
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
| | - Joshua J C Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
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3
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Mir FA, Amanullah A, Jain BP, Hyderi Z, Gautam A. Neuroepigenetics of ageing and neurodegeneration-associated dementia: An updated review. Ageing Res Rev 2023; 91:102067. [PMID: 37689143 DOI: 10.1016/j.arr.2023.102067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Gene expression is tremendously altered in the brain during memory acquisition, recall, and forgetfulness. However, non-genetic factors, including environmental elements, epigenetic changes, and lifestyle, have grabbed significant attention in recent years regarding the etiology of neurodegenerative diseases (NDD) and age-associated dementia. Epigenetic modifications are essential in regulating gene expression in all living organisms in a DNA sequence-independent manner. The genes implicated in ageing and NDD-related memory disorders are epigenetically regulated by processes such as DNA methylation, histone acetylation as well as messenger RNA editing machinery. The physiological and optimal state of the epigenome, especially within the CNS of humans, plays an intricate role in helping us adjust to the changing environment, and alterations in it cause many brain disorders, but the mechanisms behind it still need to be well understood. When fully understood, these epigenetic landscapes could act as vital targets for pharmacogenetic rescue strategies for treating several diseases, including neurodegeneration- and age-induced dementia. Keeping this objective in mind, this updated review summarises the epigenetic changes associated with age and neurodegeneration-associated dementia.
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Affiliation(s)
- Fayaz Ahmad Mir
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Zeeshan Hyderi
- Department of Biotechnology, Alagappa University, Karaikudi, India
| | - Akash Gautam
- Centre for Neural and Cognitive Sciences, University of Hyderabad, Hyderabad, India.
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4
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Mattick JS. A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs. Bioessays 2023; 45:e2300080. [PMID: 37318305 DOI: 10.1002/bies.202300080] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023]
Abstract
Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of 'normal science'. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non-functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein-coding) genes and increase in 'noncoding' sequences with developmental complexity; genetic loci termed 'enhancers' that control spatiotemporal gene expression patterns during development; and a plethora of 'intergenic', overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information. Also see the video abstract here: https://youtu.be/qxeGwahBANw.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, New South Wales, Australia
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5
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Zang J, Tang X, Su X, Zhang T, Lu D, Xu A. Systematic Analysis of RNA Expression Profiles in Different Ischemic Cortices in MCAO Mice. Cell Mol Neurobiol 2023; 43:859-878. [PMID: 35449428 DOI: 10.1007/s10571-022-01220-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/29/2022] [Indexed: 11/03/2022]
Abstract
The prognosis of ischemic stroke patients is highly associated with the collateral circulation. And the competing endogenous RNAs (ceRNAs) generated from different compensatory supply regions may also involve in the regulation of ischemic tissues prognosis. In this study, we found the apoptosis progress of ischemic neurons in posterior circulation-supplied regions (close to PCA, cortex2) was much slower than that in anterior circulation-supplied territory (close to ACA, cortex1) in MCAO-3-h mice. Using the RNA sequencing and functional enrichment analysis, we analyzed the difference between RNA expression profile in cortex1 and cortex2 and the related biological processes. The results indicated that the differential expressed ceRNAs in cortex1 were involved in cell process under acute injury, while the differential expressed ceRNAs in cortex2 was more likely to participate in long-term injury and repair process. Besides, by establishing the miRNA-ceRNA interaction network we further sorted out two specifically distributed miRNAs, namely mmu-miR446i-3p (in cortex1) and mmu-miR3473d (in cortex2). And the specifically increased mmu-miR3473d in cortex2 mainly involved the angiogenesis and cell proliferation after ischemic stroke, which may be the critical reason for the longer therapeutic time window in cortex2. In conclusion, the present study reported the specific changes of ceRNAs in distinct compensatory regions potentially involved in the evolution of cerebral ischemic tissues and the unbalance prognosis after stroke. It provided more evidence for the collateral compensatory effects on patients' prognosis and carried out the new targets for the ischemic stroke therapy.
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Affiliation(s)
- Jiankun Zang
- Department of Neurology and Stroke Center, The First Affiliated Hospital, Jinan University, 613 West Huangpu Ave, Guangzhou, 510632, China.,Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xionglin Tang
- Department of Neurology and Stroke Center, The First Affiliated Hospital, Jinan University, 613 West Huangpu Ave, Guangzhou, 510632, China.,Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xuanlin Su
- Department of Neurology and Stroke Center, The First Affiliated Hospital, Jinan University, 613 West Huangpu Ave, Guangzhou, 510632, China.,Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Tianyuan Zhang
- Department of Neurology and Stroke Center, The First Affiliated Hospital, Jinan University, 613 West Huangpu Ave, Guangzhou, 510632, China.,Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Dan Lu
- Department of Neurology and Stroke Center, The First Affiliated Hospital, Jinan University, 613 West Huangpu Ave, Guangzhou, 510632, China. .,Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Anding Xu
- Department of Neurology and Stroke Center, The First Affiliated Hospital, Jinan University, 613 West Huangpu Ave, Guangzhou, 510632, China. .,Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China.
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6
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Mattick JS. RNA out of the mist. Trends Genet 2023; 39:187-207. [PMID: 36528415 DOI: 10.1016/j.tig.2022.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022]
Abstract
RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long 'intergenic' and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed 'enhancers', which marshal generic effector proteins to their sites of action to control cell fate decisions during development.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia; UNSW RNA Institute, UNSW, Sydney, NSW 2052, Australia.
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7
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Begik O, Mattick JS, Novoa EM. Exploring the epitranscriptome by native RNA sequencing. RNA (NEW YORK, N.Y.) 2022; 28:1430-1439. [PMID: 36104106 PMCID: PMC9745831 DOI: 10.1261/rna.079404.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Chemical RNA modifications, collectively referred to as the "epitranscriptome," are essential players in fine-tuning gene expression. Our ability to analyze RNA modifications has improved rapidly in recent years, largely due to the advent of high-throughput sequencing methodologies, which typically consist of coupling modification-specific reagents, such as antibodies or enzymes, to next-generation sequencing. Recently, it also became possible to map RNA modifications directly by sequencing native RNAs using nanopore technologies, which has been applied for the detection of a number of RNA modifications, such as N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). However, the signal modulations caused by most RNA modifications are yet to be determined. A global effort is needed to determine the signatures of the full range of RNA modifications to avoid the technical biases that have so far limited our understanding of the epitranscriptome.
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Affiliation(s)
- Oguzhan Begik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra, Barcelona 08002, Spain
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8
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Chesnokova E, Beletskiy A, Kolosov P. The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology. Int J Mol Sci 2022; 23:5847. [PMID: 35628657 PMCID: PMC9148063 DOI: 10.3390/ijms23105847] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) have been extensively studied for decades. In recent years, the introduction of whole-genome and whole-transcriptome approaches, as well as single-cell resolution techniques, provided a breakthrough that uncovered TE involvement in host gene expression regulation underlying multiple normal and pathological processes. Of particular interest is increased TE activity in neuronal tissue, and specifically in the hippocampus, that was repeatedly demonstrated in multiple experiments. On the other hand, numerous neuropathologies are associated with TE dysregulation. Here, we provide a comprehensive review of literature about the role of TEs in neurons published over the last three decades. The first chapter of the present review describes known mechanisms of TE interaction with host genomes in general, with the focus on mammalian and human TEs; the second chapter provides examples of TE exaptation in normal neuronal tissue, including TE involvement in neuronal differentiation and plasticity; and the last chapter lists TE-related neuropathologies. We sought to provide specific molecular mechanisms of TE involvement in neuron-specific processes whenever possible; however, in many cases, only phenomenological reports were available. This underscores the importance of further studies in this area.
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Affiliation(s)
- Ekaterina Chesnokova
- Laboratory of Cellular Neurobiology of Learning, Institute of Higher Nervous Activity and Neurophysiology of the Russian Academy of Sciences, 117485 Moscow, Russia; (A.B.); (P.K.)
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9
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Akhlaghpour H. An RNA-Based Theory of Natural Universal Computation. J Theor Biol 2021; 537:110984. [PMID: 34979104 DOI: 10.1016/j.jtbi.2021.110984] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 09/30/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of universal computation, i.e., Turing-equivalent in scope. Generic finite-dimensional dynamical systems (which encompass most models of neural networks, intracellular signaling cascades, and gene regulatory networks) fall short of universal computation, but are assumed to be capable of explaining cognition and development. I present a class of models that bridge two concepts from distant fields: combinatory logic (or, equivalently, lambda calculus) and RNA molecular biology. A set of basic RNA editing rules can make it possible to compute any computable function with identical algorithmic complexity to that of Turing machines. The models do not assume extraordinarily complex molecular machinery or any processes that radically differ from what we already know to occur in cells. Distinct independent enzymes can mediate each of the rules and RNA molecules solve the problem of parenthesis matching through their secondary structure. In the most plausible of these models all of the editing rules can be implemented with merely cleavage and ligation operations at fixed positions relative to predefined motifs. This demonstrates that universal computation is well within the reach of molecular biology. It is therefore reasonable to assume that life has evolved - or possibly began with - a universal computer that yet remains to be discovered. The variety of seemingly unrelated computational problems across many scales can potentially be solved using the same RNA-based computation system. Experimental validation of this theory may immensely impact our understanding of memory, cognition, development, disease, evolution, and the early stages of life.
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Affiliation(s)
- Hessameddin Akhlaghpour
- Laboratory of Integrative Brain Function, The Rockefeller University, New York, NY, 10065, USA
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10
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Lezhava T, Buadze T, Mikaia N, Jokhadze T, Sigua T, Gaiozishvili M, Melkadze T. Epigenetic Activation of Ribosomal Cistrons in Chromatids of Acrocentric Chromosome 15 in Lung Cancer. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721050042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Anand H, Ende V, Singh G, Qureshi I, Duong TQ, Mehler MF. Nervous System-Systemic Crosstalk in SARS-CoV-2/COVID-19: A Unique Dyshomeostasis Syndrome. Front Neurosci 2021; 15:727060. [PMID: 34512253 PMCID: PMC8430330 DOI: 10.3389/fnins.2021.727060] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/30/2021] [Indexed: 01/05/2023] Open
Abstract
SARS-CoV-2 infection is associated with a spectrum of acute neurological syndromes. A subset of these syndromes promotes higher in-hospital mortality than is predicted by traditional parameters defining critical care illness. This suggests that deregulation of components of the central and peripheral nervous systems compromises the interplay with systemic cellular, tissue and organ interfaces to mediate numerous atypical manifestations of COVID-19 through impairments in organismal homeostasis. This unique dyshomeostasis syndrome involves components of the ACE-2/1 lifecycles, renin-angiotensin system regulatory axes, integrated nervous system functional interactions and brain regions differentially sculpted by accelerated evolutionary processes and more primordial homeostatic functions. These biological contingencies suggest a mechanistic blueprint to define long-term neurological sequelae and systemic manifestations such as premature aging phenotypes, including organ fibrosis, tissue degeneration and cancer. Therapeutic initiatives must therefore encompass innovative combinatorial agents, including repurposing FDA-approved drugs targeting components of the autonomic nervous system and recently identified products of SARS-CoV-2-host interactions.
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Affiliation(s)
- Harnadar Anand
- The Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Victoria Ende
- Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, United States
| | - Gurinder Singh
- Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, United States
| | - Irfan Qureshi
- The Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, United States
- Biohaven Pharmaceuticals, New Haven, CT, United States
| | - Tim Q. Duong
- Department of Radiology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, United States
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mark F. Mehler
- The Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, United States
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, United States
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY, United States
- Rose F. Kennedy Center for Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY, United States
- Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, United States
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
- Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY, United States
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12
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Clark K, Lee C, Gillette R, Sweedler JV. Characterization of Neuronal RNA Modifications during Non-associative Learning in Aplysia Reveals Key Roles for tRNAs in Behavioral Sensitization. ACS CENTRAL SCIENCE 2021; 7:1183-1190. [PMID: 34345669 PMCID: PMC8323240 DOI: 10.1021/acscentsci.1c00351] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Indexed: 05/12/2023]
Abstract
Subtle changes in the landscape of post-transcriptional modifications have emerged as putative regulators of central nervous system plasticity and activity-induced protein synthesis. However, simultaneous characterization of multiple RNA modifications and their covariation during learning and memory paradigms has been impeded by the complexity of animal models and lack of untargeted approaches for identifying pathway-relevant RNA modifications in small-volume samples. Here, we used mass spectrometry to profile spatiotemporal changes in dozens of neuronal RNA modifications in Aplysia californica during behavioral sensitization of a simple defensive reflex. Unique RNA modification patterns were observed in the major ganglia of trained and naı̇ve animals, with two tRNA modifications, namely, 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) and 1-methyladenosine (m1A), at significantly higher levels in trained subjects. We report that tRNAs, and their modifications, correlate with increased polyglutamine synthesis and excitability in neurons, characterizing the first link between noncoding RNA modifications and non-associative learning.
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Affiliation(s)
- Kevin
D. Clark
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Colin Lee
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Rhanor Gillette
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Molecular and Integrative Physiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Molecular and Integrative Physiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
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13
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Gold AR, Glanzman DL. The central importance of nuclear mechanisms in the storage of memory. Biochem Biophys Res Commun 2021; 564:103-113. [PMID: 34020774 DOI: 10.1016/j.bbrc.2021.04.125] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022]
Abstract
The neurobiological nature of the memory trace (engram) remains controversial. The most widely accepted hypothesis at present is that long-term memory is stored as stable, learning-induced changes in synaptic connections. This hypothesis, the synaptic plasticity hypothesis of memory, is supported by extensive experimental data gathered from over 50 years of research. Nonetheless, there are important mnemonic phenomena that the synaptic plasticity hypothesis cannot, or cannot readily, account for. Furthermore, recent work indicates that epigenetic and genomic mechanisms play heretofore underappreciated roles in memory. Here, we critically assess the evidence that supports the synaptic plasticity hypothesis and discuss alternative non-synaptic, nuclear mechanisms of memory storage, including DNA methylation and retrotransposition. We argue that long-term encoding of memory is mediated by nuclear processes; synaptic plasticity, by contrast, represents a means of relatively temporary memory storage. In addition, we propose that memories are evaluated for their mnemonic significance during an initial period of synaptic storage; if assessed as sufficiently important, the memories then undergo nuclear encoding.
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Affiliation(s)
- Adam R Gold
- Behavioral Neuroscience Program, Department of Psychology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - David L Glanzman
- Department of Integrative Biology & Physiology, UCLA College, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Department of Neurobiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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14
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Villarreal LP, Witzany G. Social Networking of Quasi-Species Consortia drive Virolution via Persistence. AIMS Microbiol 2021; 7:138-162. [PMID: 34250372 PMCID: PMC8255905 DOI: 10.3934/microbiol.2021010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.
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15
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Genomic Intelligence as Über Bio-Cybersecurity: The Gödel Sentence in Immuno-Cognitive Systems. ENTROPY 2021; 23:e23040405. [PMID: 33805411 PMCID: PMC8065710 DOI: 10.3390/e23040405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 12/27/2022]
Abstract
This paper gives formal foundations and evidence from gene science in the post Barbara McClintock era that the Gödel Sentence, far from being an esoteric construction in mathematical logic, is ubiquitous in genomic intelligence that evolved with multi-cellular life. Conditions uniquely found in the Adaptive Immune System (AIS) and Mirror Neuron System (MNS), termed the genomic immuno-cognitive system, coincide with three building blocks in computation theory of Gödel, Turing and Post (G-T-P). (i) Biotic elements have unique digital identifiers with gene codes executing 3D self-assembly for morphology and regulation of the organism using the recursive operation of Self-Ref (Self-Reference) with the other being a self-referential projection of self. (ii) A parallel offline simulation meta/mirror environment in 1–1 relation to online machine executions of self-codes gives G-T-P Self-Rep (Self-Representation). (iii) This permits a digital biotic entity to self-report that it is under attack by a biotic malware or non-self antigen in the format of the Gödel sentence, resulting in the “smarts” for contextual novelty production. The proposed unitary G-T-P recursive machinery in AIS and in MNS for social cognition yields a new explanation that the Interferon Gamma factor, known for friend-foe identification in AIS, is also integral to social behaviors. New G-T-P bio-informatics of AIS and novel anti-body production is given with interesting testable implications for COVID-19 pathology.
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16
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Schaffer AA, Levanon EY. ALU A-to-I RNA Editing: Millions of Sites and Many Open Questions. Methods Mol Biol 2021; 2181:149-162. [PMID: 32729079 DOI: 10.1007/978-1-0716-0787-9_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alu elements are repetitive short interspersed elements prevalent in the primate genome. These repeats account for over 10% of the genome with more than a million highly similar copies. A direct outcome of this is an enrichment in long structures of stable dsRNA, which are the target of adenosine deaminases acting on RNAs (ADARs), the enzymes catalyzing A-to-I RNA editing. Indeed, A-to-I editing by ADARs is extremely abundant in primates: over a hundred million editing sites exist in their genomes. However, despite the radical increase in ADAR targets brought on by the introduction of Alu elements, the few evolutionary conserved editing sites manage to retain their editing levels. Here, we review and discuss the cost of having an unusual amount of dsRNA and editing in the transcriptome, as well as the opportunities it presents, which possibly contributed to accelerating primate evolution.
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Affiliation(s)
- Amos A Schaffer
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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17
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Autism-associated miR-873 regulates ARID1B, SHANK3 and NRXN2 involved in neurodevelopment. Transl Psychiatry 2020; 10:418. [PMID: 33262327 PMCID: PMC7708977 DOI: 10.1038/s41398-020-01106-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/21/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorders (ASD) are highly heritable neurodevelopmental disorders with significant genetic heterogeneity. Noncoding microRNAs (miRNAs) are recognised as playing key roles in development of ASD albeit the function of these regulatory genes remains unclear. We previously conducted whole-exome sequencing of Australian families with ASD and identified four novel single nucleotide variations in mature miRNA sequences. A pull-down transcriptome analysis using transfected SH-SY5Y cells proposed a mechanistic model to examine changes in binding affinity associated with a unique mutation found in the conserved 'seed' region of miR-873-5p (rs777143952: T > A). Results suggested several ASD-risk genes were differentially targeted by wild-type and mutant miR-873 variants. In the current study, a dual-luciferase reporter assay confirmed miR-873 variants have a 20-30% inhibition/dysregulation effect on candidate autism risk genes ARID1B, SHANK3 and NRXN2 and also confirmed the affected expression with qPCR. In vitro mouse hippocampal neurons transfected with mutant miR-873 showed less morphological complexity and enhanced sodium currents and excitatory neurotransmission compared to cells transfected with wild-type miR-873. A second in vitro study showed CRISPR/Cas9 miR-873 disrupted SH-SY5Y neuroblastoma cells acquired a neuronal-like morphology and increased expression of ASD important genes ARID1B, SHANK3, ADNP2, ANK2 and CHD8. These results represent the first functional evidence that miR-873 regulates key neural genes involved in development and cell differentiation.
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18
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Pre-mRNA structures forming circular RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194410. [DOI: 10.1016/j.bbagrm.2019.194410] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/25/2022]
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19
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Hicks SD, Miller MW. Ethanol-induced DNA repair in neural stem cells is transforming growth factor β1-dependent. Exp Neurol 2019; 317:214-225. [PMID: 30853389 DOI: 10.1016/j.expneurol.2019.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/13/2018] [Accepted: 02/07/2019] [Indexed: 12/18/2022]
Abstract
Following neurotoxic damage, cells repair their DNA, and survive or undergo apoptosis. This study tests the hypothesis that ethanol induces a DNA damage response (DDR) in neural stem cells (NSCs) that promotes excision repair (ER) and this repair is influenced by the growth factor environment. Non-immortalized NSCs treated with fibroblast growth factor 2 or transforming growth factor (TGF) β1 were exposed to ethanol. Ethanol increased total DNA damage, reactive oxygen species, and oxidized DNA bases. TGFβ1 potentiated these toxic effects. Transcriptional analyses of cultured NSCs revealed ethanol-induced increases in transcripts related to the DDR (e.g., Hus1 and p53), base ER (e.g., Mutyh and Nthl1), and nucleotide ER (e.g., Xpc), particularly in the presence of TGFβ1. Expression and activity of ER proteins were affected by ethanol. Similar changes occurred in proliferating cells of ethanol-treated mouse fetuses. Ethanol-induced DNA repair in NSCs depends on the ambient growth factors. Gene products for DNA repair in stem cells are among the first biomarkers identifying fetal alcohol-induced damage.
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Affiliation(s)
- Steven D Hicks
- Department of Neuroscience and Physiology, State University of New York - Upstate Medical University, Syracuse, NY 13210, USA; Developmental Exposure Alcohol Research Center, Binghamton NY 13902, Cortland NY 13045, and Syracuse, NY 13210, USA
| | - Michael W Miller
- Department of Neuroscience and Physiology, State University of New York - Upstate Medical University, Syracuse, NY 13210, USA; Developmental Exposure Alcohol Research Center, Binghamton NY 13902, Cortland NY 13045, and Syracuse, NY 13210, USA; Department of Anatomy, Touro College of Osteopathic Medicine, Middletown, NY 10940, USA; Research Service, Veterans Affairs Medical Center, Syracuse, NY 13210, USA.
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20
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Marshall PR, Bredy TW. Neuroepigenetic mechanisms underlying fear extinction: emerging concepts. Psychopharmacology (Berl) 2019; 236:133-142. [PMID: 30506235 PMCID: PMC7293886 DOI: 10.1007/s00213-018-5084-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022]
Abstract
An understanding of how memory is acquired and how it can be modified in fear-related anxiety disorders, with the enhancement of failing memories on one side and a reduction or elimination of traumatic memories on the other, is a key unmet challenge in the fields of neuroscience and neuropsychiatry. The latter process depends on an important form of learning called fear extinction, where a previously acquired fear-related memory is decoupled from its ability to control behaviour through repeated non-reinforced exposure to the original fear-inducing cue. Although simple in description, fear extinction relies on a complex pattern of brain region and cell-type specific processes, some of which are unique to this form of learning and, for better or worse, contribute to the inherent instability of fear extinction memory. Here, we explore an emerging layer of biology that may compliment and enrich the synapse-centric perspective of fear extinction. As opposed to the more classically defined role of protein synthesis in the formation of fear extinction memory, a neuroepigenetic view of the experience-dependent gene expression involves an appreciation of dynamic changes in the state of the entire cell: from a transient change in plasticity at the level of the synapse, to potentially more persistent long-term effects within the nucleus. A deeper understanding of neuroepigenetic mechanisms and how they influence the formation and maintenance of fear extinction memory has the potential to enable the development of more effective treatment approaches for fear-related neuropsychiatric conditions.
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Affiliation(s)
- Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
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21
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Shevchenko G, Morris KV. All I's on the RADAR: role of ADAR in gene regulation. FEBS Lett 2018; 592:2860-2873. [PMID: 29770436 DOI: 10.1002/1873-3468.13093] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/26/2018] [Accepted: 05/05/2018] [Indexed: 12/12/2022]
Abstract
Adenosine to inosine (A-to-I) editing is the most abundant form of RNA modification in mammalian cells, which is catalyzed by adenosine deaminase acting on the double-stranded RNA (ADAR) protein family. A-to-I editing is currently known to be involved in the regulation of the immune system, RNA splicing, protein recoding, microRNA biogenesis, and formation of heterochromatin. Editing occurs within regions of double-stranded RNA, particularly within inverted Alu repeats, and is associated with many diseases including cancer, neurological disorders, and metabolic syndromes. However, the significance of RNA editing in a large portion of the transcriptome remains unknown. Here, we review the current knowledge about the prevalence and function of A-to-I editing by the ADAR protein family, focusing on its role in the regulation of gene expression. Furthermore, RNA editing-independent regulation of cellular processes by ADAR and the putative role(s) of this process in gene regulation will be discussed.
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Affiliation(s)
- Galina Shevchenko
- Hematological Malignancy and Stem Cell Transplantation Institute, Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
| | - Kevin V Morris
- Hematological Malignancy and Stem Cell Transplantation Institute, Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
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22
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Larsen PA, Hunnicutt KE, Larsen RJ, Yoder AD, Saunders AM. Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease. Chromosome Res 2018; 26:93-111. [PMID: 29460123 PMCID: PMC5857278 DOI: 10.1007/s10577-018-9573-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/14/2018] [Accepted: 01/15/2018] [Indexed: 12/28/2022]
Abstract
Alu elements are a highly successful family of primate-specific retrotransposons that have fundamentally shaped primate evolution, including the evolution of our own species. Alus play critical roles in the formation of neurological networks and the epigenetic regulation of biochemical processes throughout the central nervous system (CNS), and thus are hypothesized to have contributed to the origin of human cognition. Despite the benefits that Alus provide, deleterious Alu activity is associated with a number of neurological and neurodegenerative disorders. In particular, neurological networks are potentially vulnerable to the epigenetic dysregulation of Alu elements operating across the suite of nuclear-encoded mitochondrial genes that are critical for both mitochondrial and CNS function. Here, we highlight the beneficial neurological aspects of Alu elements as well as their potential to cause disease by disrupting key cellular processes across the CNS. We identify at least 37 neurological and neurodegenerative disorders wherein deleterious Alu activity has been implicated as a contributing factor for the manifestation of disease, and for many of these disorders, this activity is operating on genes that are essential for proper mitochondrial function. We conclude that the epigenetic dysregulation of Alu elements can ultimately disrupt mitochondrial homeostasis within the CNS. This mechanism is a plausible source for the incipient neuronal stress that is consistently observed across a spectrum of sporadic neurological and neurodegenerative disorders.
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Affiliation(s)
- Peter A Larsen
- Department of Biology, Duke University, Durham, NC, 27708, USA.
- Duke Lemur Center, Duke University, Durham, NC, 27708, USA.
- Department of Biology, Duke University, 130 Science Drive, Box 90338, Durham, NC, 27708, USA.
| | | | - Roxanne J Larsen
- Duke University School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Duke Lemur Center, Duke University, Durham, NC, 27708, USA
| | - Ann M Saunders
- Zinfandel Pharmaceuticals Inc, Chapel Hill, NC, 27709, USA
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23
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Jonkhout N, Tran J, Smith MA, Schonrock N, Mattick JS, Novoa EM. The RNA modification landscape in human disease. RNA (NEW YORK, N.Y.) 2017; 23:1754-1769. [PMID: 28855326 PMCID: PMC5688997 DOI: 10.1261/rna.063503.117] [Citation(s) in RCA: 365] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
RNA modifications have been historically considered as fine-tuning chemo-structural features of infrastructural RNAs, such as rRNAs, tRNAs, and snoRNAs. This view has changed dramatically in recent years, to a large extent as a result of systematic efforts to map and quantify various RNA modifications in a transcriptome-wide manner, revealing that RNA modifications are reversible, dynamically regulated, far more widespread than originally thought, and involved in major biological processes, including cell differentiation, sex determination, and stress responses. Here we summarize the state of knowledge and provide a catalog of RNA modifications and their links to neurological disorders, cancers, and other diseases. With the advent of direct RNA-sequencing technologies, we expect that this catalog will help prioritize those RNA modifications for transcriptome-wide maps.
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Affiliation(s)
- Nicky Jonkhout
- Garvan Institute of Medical Research, Darlinghurst, 2010 NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington NSW 2052, Australia
| | - Julia Tran
- Garvan Institute of Medical Research, Darlinghurst, 2010 NSW, Australia
| | - Martin A Smith
- Garvan Institute of Medical Research, Darlinghurst, 2010 NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington NSW 2052, Australia
| | - Nicole Schonrock
- Garvan Institute of Medical Research, Darlinghurst, 2010 NSW, Australia
- Genome.One, Darlinghurst, 2010 NSW, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, 2010 NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington NSW 2052, Australia
| | - Eva Maria Novoa
- Garvan Institute of Medical Research, Darlinghurst, 2010 NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington NSW 2052, Australia
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
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24
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Rodriguez RL, Albeck JG, Taha AY, Ori-McKenney KM, Recanzone GH, Stradleigh TW, Hernandez BC, Tang FYV, Chiang EPI, Cruz-Orengo L. Impact of diet-derived signaling molecules on human cognition: exploring the food-brain axis. NPJ Sci Food 2017; 1:2. [PMID: 31304244 PMCID: PMC6548416 DOI: 10.1038/s41538-017-0002-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 08/25/2017] [Accepted: 09/01/2017] [Indexed: 01/02/2023] Open
Abstract
The processes that define mammalian physiology evolved millions of years ago in response to ancient signaling molecules, most of which were acquired by ingestion and digestion. In this way, evolution inextricably linked diet to all major physiological systems including the nervous system. The importance of diet in neurological development is well documented, although the mechanisms by which diet-derived signaling molecules (DSMs) affect cognition are poorly understood. Studies on the positive impact of nutritive and non-nutritive bioactive molecules on brain function are encouraging but lack the statistical power needed to demonstrate strong positive associations. Establishing associations between DSMs and cognitive functions like mood, memory and learning are made even more difficult by the lack of robust phenotypic markers that can be used to accurately and reproducibly measure the effects of DSMs. Lastly, it is now apparent that processes like neurogenesis and neuroplasticity are embedded within layers of interlocked signaling pathways and gene regulatory networks. Within these interdependent pathways and networks, the various transducers of DSMs are used combinatorially to produce those emergent adaptive gene expression responses needed for stimulus-induced neurogenesis and neuroplasticity. Taken together, it appears that cognition is encoded genomically and modified by epigenetics and epitranscriptomics to produce complex transcriptional programs that are exquisitely sensitive to signaling molecules from the environment. Models for how DSMs mediate the interplay between the environment and various neuronal processes are discussed in the context of the food-brain axis.
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Affiliation(s)
- Raymond L. Rodriguez
- Department of Molecular and Cellular Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, Davis, CA 95616 USA
| | - John G. Albeck
- Department of Molecular and Cellular Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, Davis, CA 95616 USA
| | - Ameer Y. Taha
- Department of Food Science and Technology, College of Agriculture and Environmental Sciences, One Shields Avenue, University of California, Davis, Davis, CA 95616 USA
| | - Kassandra M. Ori-McKenney
- Department of Molecular and Cellular Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, Davis, CA 95616 USA
| | - Gregg H. Recanzone
- Department of Neurobiology, Physiology and Behavior, College of Biological Sciences, One Shields Avenue, University of California, Davis, Davis, CA 95616 USA
- Center for Neuroscience, College of Biological Sciences, University of California, Davis, Davis, CA 95616 USA
| | - Tyler W. Stradleigh
- Department of Neurobiology, Physiology and Behavior, College of Biological Sciences, One Shields Avenue, University of California, Davis, Davis, CA 95616 USA
- Center for Neuroscience, College of Biological Sciences, University of California, Davis, Davis, CA 95616 USA
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Bronte C. Hernandez
- Department of Molecular and Cellular Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, Davis, CA 95616 USA
| | | | - En-Pei Isabel Chiang
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Lillian Cruz-Orengo
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
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25
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Auboeuf D. Genome evolution is driven by gene expression-generated biophysical constraints through RNA-directed genetic variation: A hypothesis. Bioessays 2017; 39. [DOI: 10.1002/bies.201700069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210; Laboratory of Biology and Modelling of the Cell; Site Jacques Monod; Lyon France
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26
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Picardi E, Horner DS, Pesole G. Single-cell transcriptomics reveals specific RNA editing signatures in the human brain. RNA (NEW YORK, N.Y.) 2017; 23:860-865. [PMID: 28258159 PMCID: PMC5435858 DOI: 10.1261/rna.058271.116] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 02/21/2017] [Indexed: 06/02/2023]
Abstract
While RNA editing by A-to-I deamination is a requisite for neuronal function in humans, it is under-investigated in single cells. Here we fill this gap by analyzing RNA editing profiles of single cells from the brain cortex of living human subjects. We show that RNA editing levels per cell are bimodally distributed and distinguish between major brain cell types, thus providing new insights into neuronal dynamics.
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Affiliation(s)
- Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
- Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, Italy
| | - David S Horner
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
- Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, Italy
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27
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Chen W, An D, Xu H, Cheng X, Wang S, Yu W, Yu D, Zhao D, Sun Y, Deng W, Tang Y, Yin S. Effects of social isolation and re-socialization on cognition and ADAR1 (p110) expression in mice. PeerJ 2016; 4:e2306. [PMID: 27602277 PMCID: PMC4994079 DOI: 10.7717/peerj.2306] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 07/09/2016] [Indexed: 11/20/2022] Open
Abstract
It has been reported that social isolation stress could be a key factor that leads to cognitive deficit for both humans and rodent models. However, detailed mechanisms are not yet clear. ADAR1 (Adenosine deaminase acting on RNA) is an enzyme involved in RNA editing that has a close relation to cognitive function. We have hypothesized that social isolation stress may impact the expression of ADAR1 in the brain of mice with cognitive deficit. To test our hypothesis, we evaluated the cognition ability of mice isolated for different durations (2, 4, and 8 weeks) using object recognition and object location tests; we also measured ADAR1 expression in hippocampus and cortex using immunohistochemistry and western blot. Our study showed that social isolation stress induced spatial and non-spatial cognition deficits of the tested mice. In addition, social isolation significantly increased both the immunoreactivity and protein expression of ADAR1 (p110) in the hippocampus and frontal cortex. Furthermore, re-socialization could not only recover the cognition deficits, but also bring ADAR1 (p110) immunoreactivity of hippocampus and frontal cortex, as well as ADAR1 (p110) protein expression of hippocampus back to the normal level for the isolated mice in adolescence. In conclusion, social isolation stress significantly increases ADAR1 (p110) expression in the hippocampus and frontal cortex of the mice with cognitive deficit. This finding may open a window to better understand the reasons (e.g., epigenetic change) that are responsible for social isolation-induced cognitive deficit and help the development of novel therapies for the resulted diseases.
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Affiliation(s)
- Wei Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Dong An
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Hong Xu
- Department of Physiology Laboratory, Dalian Medical University, Dalian, China
| | - Xiaoxin Cheng
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Shiwei Wang
- Menzies Research Institute, University of Tasmania, Tasmania, Australia
| | - Weizhi Yu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Deqin Yu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Dan Zhao
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yiping Sun
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Wuguo Deng
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yiyuan Tang
- Department of Psychological Sciences, Texas Tech University, Lubbock, United States
| | - Shengming Yin
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
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28
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Abstract
Understanding the molecular mechanisms behind the capacity of cancer cells to adapt to the tumor microenvironment and to anticancer therapies is a major challenge. In this context, cancer is believed to be an evolutionary process where random mutations and the selection process shape the mutational pattern and phenotype of cancer cells. This article challenges the notion of randomness of some cancer-associated mutations by describing molecular mechanisms involving stress-mediated biogenesis of mRNA-derived small RNAs able to target and increase the local mutation rate of the genomic loci they originate from. It is proposed that the probability of some mutations at specific loci could be increased in a stress-specific and RNA-depending manner. This would increase the probability of generating mutations that could alleviate stress situations, such as those triggered by anticancer drugs. Such a mechanism is made possible because tumor- and anticancer drug-associated stress situations trigger both cellular reprogramming and inflammation, which leads cancer cells to express molecular tools allowing them to “attack” and mutate their own genome in an RNA-directed manner.
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Affiliation(s)
- Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
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29
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Coskun AF, Eser U, Islam S. Cellular identity at the single-cell level. MOLECULAR BIOSYSTEMS 2016; 12:2965-79. [PMID: 27460751 DOI: 10.1039/c6mb00388e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A single cell creates surprising heterogeneity in a multicellular organism. While every organismal cell shares almost an identical genome, molecular interactions in cells alter the use of DNA sequences to modulate the gene of interest for specialization of cellular functions. Each cell gains a unique identity through molecular coding across the DNA, RNA, and protein conversions. On the other hand, loss of cellular identity leads to critical diseases such as cancer. Most cell identity dissection studies are based on bulk molecular assays that mask differences in individual cells. To probe cell-to-cell variability in a population, we discuss single cell approaches to decode the genetic, epigenetic, transcriptional, and translational mechanisms for cell identity formation. In combination with molecular instructions, the physical principles behind cell identity determination are examined. Deciphering and reprogramming cellular types impact biology and medicine.
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Affiliation(s)
- Ahmet F Coskun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, California, USA.
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30
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Marshall P, Bredy TW. Cognitive neuroepigenetics: the next evolution in our understanding of the molecular mechanisms underlying learning and memory? NPJ SCIENCE OF LEARNING 2016; 1:16014. [PMID: 27512601 PMCID: PMC4977095 DOI: 10.1038/npjscilearn.2016.14] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/02/2016] [Accepted: 06/21/2016] [Indexed: 05/02/2023]
Abstract
A complete understanding of the fundamental mechanisms of learning and memory continues to elude neuroscientists. Although many important discoveries have been made, the question of how memories are encoded and maintained at the molecular level remains. To date, this issue has been framed within the context of one of the most dominant concepts in molecular biology, the central dogma, and the result has been a protein-centric view of memory. Here we discuss the evidence supporting a role for neuroepigenetic mechanisms, which constitute dynamic and reversible, state-dependent modifications at all levels of control over cellular function, and their role in learning and memory. This neuroepigenetic view suggests that DNA, RNA and protein each influence one another to produce a holistic cellular state that contributes to the formation and maintenance of memory, and predicts a parallel and distributed system for the consolidation, storage and retrieval of the engram.
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Affiliation(s)
- Paul Marshall
- Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, USA
| | - Timothy W Bredy
- Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, USA
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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31
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Wüllner U, Kaut O, deBoni L, Piston D, Schmitt I. DNA methylation in Parkinson's disease. J Neurochem 2016; 139 Suppl 1:108-120. [DOI: 10.1111/jnc.13646] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/21/2016] [Accepted: 04/15/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Ullrich Wüllner
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Oliver Kaut
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Laura deBoni
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Dominik Piston
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Ina Schmitt
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
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32
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Abstract
The transfer of genetic information from RNA to DNA is considered an extraordinary process in molecular biology. Despite the fact that cells transcribe abundant amount of RNA with a wide range of functions, it has been difficult to uncover whether RNA can serve as a template for DNA repair and recombination. An increasing number of experimental evidences suggest a direct role of RNA in DNA modification. Recently, we demonstrated that endogenous transcript RNA can serve as a template to repair a DNA double-strand break (DSB), the most harmful DNA lesion, not only indirectly via formation of a DNA copy (cDNA) intermediate, but also directly in a homology driven mechanism in budding yeast. These results point out that the transfer of genetic information from RNA to DNA is more general than previously thought. We found that transcript RNA is more efficient in repairing a DSB in its own DNA (in cis) than in a homologous but ectopic locus (in trans). Here, we summarize current knowledge about the process of RNA-driven DNA repair and recombination, and provide further data in support of our model of DSB repair by transcript RNA in cis. We show that a DSB is precisely repaired predominately by transcript RNA and not by residual cDNA in conditions in which formation of cDNA by reverse transcription is inhibited. Additionally, we demonstrate that defects in ribonuclease (RNase) H stimulate precise DSB repair by homologous RNA or cDNA sequence, and not by homologous DNA sequence carried on a plasmid. These results highlight an antagonistic role of RNase H in RNA-DNA recombination. Ultimately, we discuss several questions that should be addressed to better understand mechanisms and implications of RNA-templated DNA repair and recombination.
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Affiliation(s)
- Havva Keskin
- a School of Biology, Georgia Institute of Technology , Atlanta , Georgia , USA
| | - Chance Meers
- a School of Biology, Georgia Institute of Technology , Atlanta , Georgia , USA
| | - Francesca Storici
- a School of Biology, Georgia Institute of Technology , Atlanta , Georgia , USA
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Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution. Neuron 2015; 88:861-877. [DOI: 10.1016/j.neuron.2015.09.045] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Liscovitch N, Bazak L, Levanon EY, Chechik G. Positive correlation between ADAR expression and its targets suggests a complex regulation mediated by RNA editing in the human brain. RNA Biol 2015; 11:1447-56. [PMID: 25692240 DOI: 10.4161/15476286.2014.992286] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A-to-I RNA editing by adenosine deaminases acting on RNA is a post-transcriptional modification that is crucial for normal life and development in vertebrates. RNA editing has been shown to be very abundant in the human transcriptome, specifically at the primate-specific Alu elements. The functional role of this wide-spread effect is still not clear; it is believed that editing of transcripts is a mechanism for their down-regulation via processes such as nuclear retention or RNA degradation. Here we combine 2 neural gene expression datasets with genome-level editing information to examine the relation between the expression of ADAR genes with the expression of their target genes. Specifically, we computed the spatial correlation across structures of post-mortem human brains between ADAR and a large set of targets that were found to be edited in their Alu repeats. Surprisingly, we found that a large fraction of the edited genes are positively correlated with ADAR, opposing the assumption that editing would reduce expression. When considering the correlations between ADAR and its targets over development, 2 gene subsets emerge, positively correlated and negatively correlated with ADAR expression. Specifically, in embryonic time points, ADAR is positively correlated with many genes related to RNA processing and regulation of gene expression. These findings imply that the suggested mechanism of regulation of expression by editing is probably not a global one; ADAR expression does not have a genome wide effect reducing the expression of editing targets. It is possible, however, that RNA editing by ADAR in non-coding regions of the gene might be a part of a more complex expression regulation mechanism.
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Affiliation(s)
- Noa Liscovitch
- a Gonda Multidisiplinary Brain Research Center ; Bar-Ilan University ; Ramat Gan , Israel
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35
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Caudron-Herger M, Pankert T, Seiler J, Németh A, Voit R, Grummt I, Rippe K. Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 2015; 34:2758-74. [PMID: 26464461 DOI: 10.15252/embj.201591458] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023] Open
Abstract
Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production.
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Affiliation(s)
- Maïwen Caudron-Herger
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Teresa Pankert
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Jeanette Seiler
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Attila Németh
- Department of Biochemistry III, Biochemistry Center Regensburg University of Regensburg, Regensburg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Karsten Rippe
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
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36
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Maag JLV, Panja D, Sporild I, Patil S, Kaczorowski DC, Bramham CR, Dinger ME, Wibrand K. Dynamic expression of long noncoding RNAs and repeat elements in synaptic plasticity. Front Neurosci 2015; 9:351. [PMID: 26483626 PMCID: PMC4589673 DOI: 10.3389/fnins.2015.00351] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/16/2015] [Indexed: 01/29/2023] Open
Abstract
Long-term potentiation (LTP) of synaptic transmission is recognized as a cellular mechanism for learning and memory storage. Although de novo gene transcription is known to be required in the formation of stable LTP, the molecular mechanisms underlying synaptic plasticity remain elusive. Noncoding RNAs have emerged as major regulatory molecules that are abundantly and specifically expressed in the mammalian brain. By combining RNA-seq analysis with LTP induction in the dentate gyrus of live rats, we provide the first global transcriptomic analysis of synaptic plasticity in the adult brain. Expression profiles of mRNAs and long noncoding RNAs (lncRNAs) were obtained at 30 min, 2 and 5 h after high-frequency stimulation of the perforant pathway. The temporal analysis revealed dynamic expression profiles of lncRNAs with many positively, and highly, correlated to protein-coding genes with known roles in synaptic plasticity, suggesting their possible involvement in LTP. In light of observations suggesting a role for retrotransposons in brain function, we examined the expression of various classes of repeat elements. Our analysis identifies dynamic regulation of LINE1 and SINE retrotransposons, and extensive regulation of tRNA. These experiments reveal a hitherto unknown complexity of gene expression in long-term synaptic plasticity involving the dynamic regulation of lncRNAs and repeat elements. These findings provide a broader foundation for elucidating the transcriptional and epigenetic regulation of synaptic plasticity in both the healthy brain and in neurodegenerative and neuropsychiatric disorders.
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Affiliation(s)
- Jesper L V Maag
- Genomics and Epigenetics Division, Garvan Institute of Medical Research Sydney, NSW, Australia ; Faculty of Medicine, St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Debabrata Panja
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| | - Ida Sporild
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| | - Sudarshan Patil
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| | - Dominik C Kaczorowski
- Genomics and Epigenetics Division, Garvan Institute of Medical Research Sydney, NSW, Australia
| | - Clive R Bramham
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| | - Marcel E Dinger
- Genomics and Epigenetics Division, Garvan Institute of Medical Research Sydney, NSW, Australia ; Faculty of Medicine, St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Karin Wibrand
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
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Lardenoije R, Iatrou A, Kenis G, Kompotis K, Steinbusch HWM, Mastroeni D, Coleman P, Lemere CA, Hof PR, van den Hove DLA, Rutten BPF. The epigenetics of aging and neurodegeneration. Prog Neurobiol 2015; 131:21-64. [PMID: 26072273 PMCID: PMC6477921 DOI: 10.1016/j.pneurobio.2015.05.002] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/14/2022]
Abstract
Epigenetics is a quickly growing field encompassing mechanisms regulating gene expression that do not involve changes in the genotype. Epigenetics is of increasing relevance to neuroscience, with epigenetic mechanisms being implicated in brain development and neuronal differentiation, as well as in more dynamic processes related to cognition. Epigenetic regulation covers multiple levels of gene expression; from direct modifications of the DNA and histone tails, regulating the level of transcription, to interactions with messenger RNAs, regulating the level of translation. Importantly, epigenetic dysregulation currently garners much attention as a pivotal player in aging and age-related neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, where it may mediate interactions between genetic and environmental risk factors, or directly interact with disease-specific pathological factors. We review current knowledge about the major epigenetic mechanisms, including DNA methylation and DNA demethylation, chromatin remodeling and non-coding RNAs, as well as the involvement of these mechanisms in normal aging and in the pathophysiology of the most common neurodegenerative diseases. Additionally, we examine the current state of epigenetics-based therapeutic strategies for these diseases, which either aim to restore the epigenetic homeostasis or skew it to a favorable direction to counter disease pathology. Finally, methodological challenges of epigenetic investigations and future perspectives are discussed.
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Affiliation(s)
- Roy Lardenoije
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Artemis Iatrou
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Gunter Kenis
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Konstantinos Kompotis
- Center for Integrative Genomics, University of Lausanne, Genopode Building, 1015 Lausanne-Dorigny, Switzerland
| | - Harry W M Steinbusch
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Diego Mastroeni
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands; L.J. Roberts Alzheimer's Disease Center, Banner Sun Health Research Institute, 10515 W. Santa Fe Drive, Sun City, AZ 85351, USA
| | - Paul Coleman
- L.J. Roberts Alzheimer's Disease Center, Banner Sun Health Research Institute, 10515 W. Santa Fe Drive, Sun City, AZ 85351, USA
| | - Cynthia A Lemere
- Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Daniel L A van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands; Laboratory of Translational Neuroscience, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Fuechsleinstrasse 15, 97080 Wuerzburg, Germany
| | - Bart P F Rutten
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands.
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Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response. Sci Rep 2015. [PMID: 26223940 PMCID: PMC4519770 DOI: 10.1038/srep12615] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We recently showed that spinal cord injury (SCI) leads to a decrease in mRNA editing of serotonin receptor 2C (5-HT2CR) contributing to post-SCI spasticity. Here we study post-SCI mRNA editing and global gene expression using massively parallel sequencing. Evidence is presented that the decrease in 5-HT2CR editing is caused by down-regulation of adenosine deaminase ADAR2 and that editing of at least one other ADAR2 target, potassium channel Kv1.1, is decreased after SCI. Bayesian network analysis of genome-wide transcriptome data indicates that down-regulation of ADAR2 (1) is triggered by persistent inflammatory response to SCI that is associated with activation of microglia and (2) results in changes in neuronal gene expression that are likely to contribute both to post-SCI restoration of neuronal excitability and muscle spasms. These findings have broad implications for other diseases of the Central Nervous System and could open new avenues for developing efficacious antispastic treatments.
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Karanović J, Šviković S, Pantović M, Durica S, Brajušković G, Damjanović A, Jovanović V, Ivković M, Romac S, Savić Pavićević D. Joint effect of ADARB1 gene, HTR2C gene and stressful life events on suicide attempt risk in patients with major psychiatric disorders. World J Biol Psychiatry 2015; 16:261-71. [PMID: 25732952 DOI: 10.3109/15622975.2014.1000374] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVES Adenosine to inosine RNA editing, serotonin 2C receptor (HTR2C), and stressful life events (SLEs) have all been implicated in suicidal behaviour. We examined the main and moderating effects of RNA editing (ADAR, ADARB1) and HTR2C genes, childhood trauma (CT), recent SLEs and psychiatric disorders as contributors to suicide attempt (SA) vulnerability. METHODS Study included 165 suicide attempters and 188 suicide non-attempters, all diagnosed with one of major psychiatric disorders. CT and recent SLEs were assessed using Early Trauma Inventory-Self Report and List of Threatening Experiences Questionnaire, respectively. Selected ADAR and ADARB1 tag-variants, and HTR2C rs6318 were pre-screened for association with SA, while generalized linear models and backward selection were applied to identify individual and interacting SA risk factors. RESULTS ADARB1 rs9983925 and rs4819035 and HTR2C rs6318 were associated with SA. The best minimal model found emotional abuse, recent SLEs, rs9983925 and rs6318 as independent SA risk factors, and general traumas as a factor moderating the effect of psychiatric disorders and emotional abuse. CONCLUSIONS SA vulnerability in psychiatric patients is related to the joint effect of ADARB1 and HTR2C variants, the existing mood disorder and the cumulative exposures to a various childhood and recent stressful experiences.
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Affiliation(s)
- Jelena Karanović
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade , Belgrade , Serbia
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Knisbacher BA, Levanon EY. DNA and RNA editing of retrotransposons accelerate mammalian genome evolution. Ann N Y Acad Sci 2015; 1341:115-25. [PMID: 25722083 DOI: 10.1111/nyas.12713] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genome evolution is commonly viewed as a gradual process that is driven by random mutations that accumulate over time. However, DNA- and RNA-editing enzymes have been identified that can accelerate evolution by actively modifying the genomically encoded information. The apolipoprotein B mRNA editing enzymes, catalytic polypeptide-like (APOBECs) are potent restriction factors that can inhibit retroelements by cytosine-to-uridine editing of retroelement DNA after reverse transcription. In some cases, a retroelement may successfully integrate into the genome despite being hypermutated. Such events introduce unique sequences into the genome and are thus a source of genomic innovation. adenosine deaminases that act on RNA (ADARs) catalyze adenosine-to-inosine editing in double-stranded RNA, commonly formed by oppositely oriented retroelements. The RNA editing confers plasticity to the transcriptome by generating many transcript variants from a single genomic locus. If the editing produces a beneficial variant, the genome may maintain the locus that produces the RNA-edited transcript for its novel function. Here, we discuss how these two powerful editing mechanisms, which both target inserted retroelements, facilitate expedited genome evolution.
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Affiliation(s)
- Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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41
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Abstract
One of the distinctive features of the primate genome is the Alu element, a repetitive short interspersed element, over a million highly similar copies of which account for >10% of the genome. A direct consequence of this feature is that primates' transcriptome is highly enriched in long stable dsRNA structures, the preferred target of adenosine deaminases acting on RNAs (ADARs), which are the enzymes catalyzing A-to-I RNA editing. Indeed, A-to-I editing by ADARs is extremely abundant in primates: over a hundred million editing sites exist in their genomes. However, there are few essential editing sites conserved across mammals that have maintained their editing level despite the radical change in ADAR target landscape. Here, we review and discuss the cost of having an unusual amount of dsRNA and editing in the transcriptome, as well as the opportunities it presents, which might have contributed to the accelerated evolution of the primates.
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Affiliation(s)
- Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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Cao J. The functional role of long non-coding RNAs and epigenetics. Biol Proced Online 2014; 16:11. [PMID: 25276098 PMCID: PMC4177375 DOI: 10.1186/1480-9222-16-11] [Citation(s) in RCA: 249] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/06/2014] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition that lncRNAs make effects in many biological and pathological processes such as stem cell pluripotency, neurogenesis, oncogenesis and etc. This review will focus on the functional roles of lncRNAs in epigenetics and related research progress will be summarized.
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Affiliation(s)
- Jinneng Cao
- Department of respiratory medicine, Fuyong People's Hospital, Baoan District, Shenzhen 518103, Guangdong, People's Republic of China
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43
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Cîrneci D, Silaghi-Dumitrescu R. Learning tasks as a possible treatment for DNA lesions induced by oxidative stress in hippocampal neurons. Neural Regen Res 2014; 8:3063-70. [PMID: 25206627 PMCID: PMC4146205 DOI: 10.3969/j.issn.1673-5374.2013.32.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/26/2013] [Indexed: 11/18/2022] Open
Abstract
Reactive oxygen species have been implicated in conditions ranging from cardiovascular dysfunc-tion, arthritis, cancer, to aging and age-related disorders. The organism developed several path-ways to counteract these effects, with base excision repair being responsible for repairing one of the major base lesions (8-oxoG) in all organisms. Epidemiological evidence suggests that cognitive stimulation makes the brain more resilient to damage or degeneration. Recent studies have linked enriched environment to reduction of oxidative stressin neurons of mice with Alzheimer's dis-ease-like disease, but given its complexity it is not clear what specific aspect of enriched environ-ment has therapeutic effects. Studies from molecular biology have shown that the protein p300, which is a transcription co-activator required for consolidation of memories during specific learning tasks, is at the same time involved in DNA replication and repair, playing a central role in the long-patch pathway of base excision repair. Based on the evidence, we propose that learning tasks such as novel object recognition could be tested as possible methods of base excision repair faci-litation, hence inducing DNA repair in the hippocampal neurons. If this method proves to be effective, it could be the start for designing similar tasks for humans, as a behavioral therapeutic complement to the classical drug-based therapy in treating neurodegenerative disorders. This review presents the current status of therapeutic methods used in treating neurodegenerative diseases induced by reactive oxygen species and proposes a new approach based on existing data.
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Affiliation(s)
- Dragoş Cîrneci
- Brain Research Institute, Synergon Consulting, Bucharest 010094, Romania
| | - Radu Silaghi-Dumitrescu
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj Napoca, 400165, Romania
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Chen M, He X, Wang K, He D, Yang X, Shi H. Inorganic fluorescent nanoprobes for cellular and subcellular imaging. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.03.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Di Narzo AF, Kozlenkov A, Roussos P, Hao K, Hurd Y, Lewis DA, Sibille E, Siever LJ, Koonin E, Dracheva S. A unique gene expression signature associated with serotonin 2C receptor RNA editing in the prefrontal cortex and altered in suicide. Hum Mol Genet 2014; 23:4801-13. [PMID: 24781207 DOI: 10.1093/hmg/ddu195] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Editing of the pre-mRNA for the serotonin receptor 2C (5-HT2CR) by site-specific adenosine deamination (A-to-I pre-mRNA editing) substantially increases the functional plasticity of this key neurotransmitter receptor and is thought to contribute to homeostatic mechanisms in neurons. 5-HT2CR mRNA editing generates up to 24 different receptor isoforms. The extent of editing correlates with 5-HT2CR functional activity: more highly edited isoforms exhibit the least function. Altered 5-HT2CR editing has been reported in postmortem brains of suicide victims. We report a comparative analysis of the connections among 5-HT2CR editing, genome-wide gene expression and DNA methylation in suicide victims, individuals with major depressive disorder and non-psychiatric controls. The results confirm previous findings of an overrepresentation of highly edited mRNA variants (which encode hypoactive 5-HT2CR receptors) in the brains of suicide victims. A large set of genes for which the expression level is associated with editing was detected. This signature set of editing-associated genes is significantly enriched for genes that are involved in synaptic transmission, genes that are preferentially expressed in neurons, and genes whose expression is correlated with the level of DNA methylation. Notably, we report that the link between 5-HT2CR editing and gene expression is disrupted in suicide victims. The results suggest that the postulated homeostatic function of 5-HT2CR editing is dysregulated in individuals who committed suicide.
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Affiliation(s)
| | - Alexey Kozlenkov
- Department of Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA James J. Peters VA Medical Center, Bronx, NY, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences and Department of Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA James J. Peters VA Medical Center, Bronx, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences and
| | - Yasmin Hurd
- Department of Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David A Lewis
- Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Etienne Sibille
- Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Larry J Siever
- Department of Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA James J. Peters VA Medical Center, Bronx, NY, USA
| | - Eugene Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Stella Dracheva
- Department of Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA James J. Peters VA Medical Center, Bronx, NY, USA
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Shine JM, Shine R. Delegation to automaticity: the driving force for cognitive evolution? Front Neurosci 2014; 8:90. [PMID: 24808820 PMCID: PMC4010745 DOI: 10.3389/fnins.2014.00090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 04/09/2014] [Indexed: 11/30/2022] Open
Abstract
The ability to delegate control over repetitive tasks from higher to lower neural centers may be a fundamental innovation in human cognition. Plausibly, the massive neurocomputational challenges associated with the mastery of balance during the evolution of bipedality in proto-humans provided a strong selective advantage to individuals with brains capable of efficiently transferring tasks in this way. Thus, the shift from quadrupedal to bipedal locomotion may have driven the rapid evolution of distinctive features of human neuronal functioning. We review recent studies of functional neuroanatomy that bear upon this hypothesis, and identify ways to test our ideas.
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Affiliation(s)
- J. M. Shine
- Brain and Mind Research Institute, The University of SydneySydney, NSW, Australia
| | - R. Shine
- School of Biological Sciences, The University of SydneySydney, NSW, Australia
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47
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Avesson L, Barry G. The emerging role of RNA and DNA editing in cancer. Biochim Biophys Acta Rev Cancer 2014; 1845:308-16. [PMID: 24607277 DOI: 10.1016/j.bbcan.2014.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/25/2014] [Accepted: 03/01/2014] [Indexed: 12/22/2022]
Abstract
UNLABELLED Nucleotide sequence modification through single base editing in animals is emerging as an important player in tumorigenesis. RNA editing especially has increased greatly during mammalian evolution and modulates diverse cellular functions presumably in a context-dependent manner. Sequence editing impacts development, including pluripotency and hematopoiesis, and multiple recent studies have shown that dysregulation of editing is associated with tumor biology. Much is yet to be learned about the role of sequence editing in human biology but this process is a critical modulator of cell regulation and may present an attractive option for therapeutic intervention in cancer in the future. SIGNIFICANCE Sequence editing provides an additional regulatory layer of cancer initiation and progression that may be amenable to therapeutic design. Although editing of both RNA and DNA substrates has been known to occur for some time, the extent and implications of these modifications have been grossly underappreciated until recent genome-wide and disease-association studies were reported. This review highlights the cellular processes controlled by sequence editing, their implications in normal and cancerous states and considers potential targeted therapeutic strategies.
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Affiliation(s)
- Lotta Avesson
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Guy Barry
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
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48
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Abstract
Alus are transposable elements belonging to the short interspersed element family. They occupy over 10% of human genome and have been spreading through genomes over the past 65 million years. In the past, they were considered junk DNA with little function that took up genome volumes. Today, Alus and other transposable elements emerge to be key players in cellular function, including genomic activities, gene expression regulations, and evolution. Here we summarize the current understanding of Alu function in genome and gene expression regulation in human cell nuclei.
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Affiliation(s)
- Chen Wang
- Department of Cell and Molecular Biology; Northwestern University; Feinberg School of Medicine; Chicago, IL USA
| | - Sui Huang
- Department of Cell and Molecular Biology; Northwestern University; Feinberg School of Medicine; Chicago, IL USA
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Barry G. Lamarckian evolution explains human brain evolution and psychiatric disorders. Front Neurosci 2013; 7:224. [PMID: 24324395 PMCID: PMC3840504 DOI: 10.3389/fnins.2013.00224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 11/05/2013] [Indexed: 01/05/2023] Open
Affiliation(s)
- Guy Barry
- Neuroscience Division, Garvan Institute of Medical Research Darlinghurst, NSW, Australia
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